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Calcium in PDB 1d2v: Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5

Enzymatic activity of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5

All present enzymatic activity of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5, PDB code: 1d2v was solved by T.J.Fiedler, C.A.Davey, R.E.Fenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.155, 63.488, 92.476, 90.00, 97.36, 90.00
R / Rfree (%) 24.3 / 29.6

Other elements in 1d2v:

The structure of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 also contains other interesting chemical elements:

Bromine (Br) 8 atoms
Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 (pdb code 1d2v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5, PDB code: 1d2v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1d2v

Go back to Calcium Binding Sites List in 1d2v
Calcium binding site 1 out of 2 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca600

b:5.4
occ:1.00
O C:PHE170 2.3 2.2 1.0
O A:ASP96 2.4 2.7 1.0
OD1 C:ASP172 2.4 3.3 1.0
OG1 C:THR168 2.5 2.0 1.0
O C:THR168 2.5 2.7 1.0
OD2 A:ASP96 2.5 4.1 1.0
OG C:SER174 2.6 2.0 1.0
CG C:ASP172 3.4 5.5 1.0
CB C:SER174 3.4 4.3 1.0
C A:ASP96 3.4 3.1 1.0
C C:THR168 3.4 3.6 1.0
C C:PHE170 3.5 5.1 1.0
CG A:ASP96 3.7 6.3 1.0
CB C:THR168 3.8 3.3 1.0
OD2 C:ASP172 3.8 5.9 1.0
N C:PHE170 3.9 3.7 1.0
CA C:THR168 4.1 4.3 1.0
CA A:ASP96 4.1 2.0 1.0
C C:SER169 4.1 4.6 1.0
N C:ASP172 4.1 4.0 1.0
N C:SER174 4.2 4.6 1.0
CA C:PHE170 4.2 4.7 1.0
N C:THR168 4.3 3.4 1.0
CB A:ASP96 4.3 4.7 1.0
O C:SER169 4.4 2.9 1.0
N C:SER169 4.4 4.0 1.0
CA C:SER174 4.4 3.7 1.0
N A:LEU97 4.5 3.1 1.0
O C:HOH690A 4.5 3.6 1.0
N C:VAL171 4.5 5.5 1.0
CB C:ASP172 4.6 5.2 1.0
CA C:SER169 4.7 5.9 1.0
CA A:LEU97 4.7 5.4 1.0
OD1 A:ASP96 4.7 2.1 1.0
CA C:VAL171 4.8 5.1 1.0
CA C:ASP172 4.8 3.4 1.0
CG2 C:THR168 4.8 2.0 1.0
CB C:PHE170 4.8 4.6 1.0
N C:ALA173 4.9 4.1 1.0
C C:VAL171 5.0 5.1 1.0

Calcium binding site 2 out of 2 in 1d2v

Go back to Calcium Binding Sites List in 1d2v
Calcium binding site 2 out of 2 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca600

b:7.7
occ:1.00
O B:ASP96 2.3 3.3 1.0
O D:PHE170 2.3 2.8 1.0
OD1 D:ASP172 2.4 6.3 1.0
OG1 D:THR168 2.5 4.0 1.0
O D:THR168 2.5 5.8 1.0
OD2 B:ASP96 2.5 6.4 1.0
OG D:SER174 2.5 5.4 1.0
C D:THR168 3.3 5.5 1.0
C B:ASP96 3.4 4.2 1.0
CB D:SER174 3.4 7.6 1.0
CG D:ASP172 3.5 10.2 1.0
C D:PHE170 3.5 3.3 1.0
CG B:ASP96 3.7 8.0 1.0
CB D:THR168 3.7 6.2 1.0
OD2 D:ASP172 3.9 10.6 1.0
N D:PHE170 3.9 4.9 1.0
CA D:THR168 4.0 6.6 1.0
C D:SER169 4.1 6.4 1.0
CA B:ASP96 4.1 4.6 1.0
N D:SER174 4.2 8.1 1.0
N D:ASP172 4.2 8.4 1.0
CA D:PHE170 4.3 4.6 1.0
N D:SER169 4.3 8.2 1.0
N D:THR168 4.3 5.3 1.0
O D:SER169 4.4 4.0 1.0
CB B:ASP96 4.4 5.4 1.0
CA D:SER174 4.4 7.9 1.0
N B:LEU97 4.5 3.0 1.0
O D:HOH690B 4.5 2.2 1.0
N D:VAL171 4.6 4.0 1.0
CA D:SER169 4.6 8.8 1.0
OD1 B:ASP96 4.6 5.8 1.0
CA B:LEU97 4.7 5.3 1.0
CB D:ASP172 4.7 8.1 1.0
CA D:VAL171 4.8 5.8 1.0
CG2 D:THR168 4.8 4.6 1.0
CB D:PHE170 4.8 4.0 1.0
CA D:ASP172 4.9 8.5 1.0

Reference:

T.J.Fiedler, C.A.Davey, R.E.Fenna. X-Ray Crystal Structure and Characterization of Halide-Binding Sites of Human Myeloperoxidase at 1.8 A Resolution. J.Biol.Chem. V. 275 11964 2000.
ISSN: ISSN 0021-9258
PubMed: 10766826
DOI: 10.1074/JBC.275.16.11964
Page generated: Sat Dec 12 02:52:23 2020

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